PlantTribes: a gene and gene family resource for comparative genomics in plants

The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm...

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Main Authors:	Wall, P. Kerr, Leebens-Mack, Jim, Müller, Kai F., Field, Dawn, Altman, Naomi S., dePamphilis, Claude W.
Format:	Online
Language:	English
Published:	Oxford University Press 2008
Online Access:	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238917/

id	pubmed-2238917
recordtype	oai_dc
spelling	pubmed-22389172008-02-12 PlantTribes: a gene and gene family resource for comparative genomics in plants Wall, P. Kerr Leebens-Mack, Jim Müller, Kai F. Field, Dawn Altman, Naomi S. dePamphilis, Claude W. Articles The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting ∼4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study. Oxford University Press 2008-01 2007-12-10 /pmc/articles/PMC2238917/ /pubmed/18073194 http://dx.doi.org/10.1093/nar/gkm972 Text en © 2007 The Author(s) http://creativecommons.org/licenses/by-nc/2.0/uk/ This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
repository_type	Open Access Journal
institution_category	Foreign Institution
institution	US National Center for Biotechnology Information
building	NCBI PubMed
collection	Online Access
language	English
format	Online
author	Wall, P. Kerr Leebens-Mack, Jim Müller, Kai F. Field, Dawn Altman, Naomi S. dePamphilis, Claude W.
spellingShingle	Wall, P. Kerr Leebens-Mack, Jim Müller, Kai F. Field, Dawn Altman, Naomi S. dePamphilis, Claude W. PlantTribes: a gene and gene family resource for comparative genomics in plants
author_facet	Wall, P. Kerr Leebens-Mack, Jim Müller, Kai F. Field, Dawn Altman, Naomi S. dePamphilis, Claude W.
author_sort	Wall, P. Kerr
title	PlantTribes: a gene and gene family resource for comparative genomics in plants
title_short	PlantTribes: a gene and gene family resource for comparative genomics in plants
title_full	PlantTribes: a gene and gene family resource for comparative genomics in plants
title_fullStr	PlantTribes: a gene and gene family resource for comparative genomics in plants
title_full_unstemmed	PlantTribes: a gene and gene family resource for comparative genomics in plants
title_sort	planttribes: a gene and gene family resource for comparative genomics in plants
description	The PlantTribes database (http://fgp.huck.psu.edu/tribe.html) is a plant gene family database based on the inferred proteomes of five sequenced plant species: Arabidopsis thaliana, Carica papaya, Medicago truncatula, Oryza sativa and Populus trichocarpa. We used the graph-based clustering algorithm MCL [Van Dongen (Technical Report INS-R0010 2000) and Enright et al. (Nucleic Acids Res. 2002; 30: 1575–1584)] to classify all of these species’ protein-coding genes into putative gene families, called tribes, using three clustering stringencies (low, medium and high). For all tribes, we have generated protein and DNA alignments and maximum-likelihood phylogenetic trees. A parallel database of microarray experimental results is linked to the genes, which lets researchers identify groups of related genes and their expression patterns. Unified nomenclatures were developed, and tribes can be related to traditional gene families and conserved domain identifiers. SuperTribes, constructed through a second iteration of MCL clustering, connect distant, but potentially related gene clusters. The global classification of nearly 200 000 plant proteins was used as a scaffold for sorting ∼4 million additional cDNA sequences from over 200 plant species. All data and analyses are accessible through a flexible interface allowing users to explore the classification, to place query sequences within the classification, and to download results for further study.
publisher	Oxford University Press
publishDate	2008
url	https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238917/
_version_	1611438803858227200

PlantTribes: a gene and gene family resource for comparative genomics in plants

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